Avery's Journey Begins
by CrayChic15
Summary: A retelling of the events of Mass Effect 1 with a blend of AU and some canon elements. Slow-build romance between Avery Shepard and Joker. Sequel to "Subject Alpha".
1. Chapter 1

**Chapter 1**

Humanity has been given a chance to have one of their own join the ranks of the SPECTRES, the Special Tactics and Reconnaissance branch of the Council. A great opportunity that places humanity one step closer to finally having a seat on that same Council. For Ambassador Donnel Udina, it now put him one step closer to gaining the power he felt that he deserved.

Admiral Hackett and Captain Anderson were currently meeting with the Ambassador discussing SPECTRE candidates. The list was short, only three names: Lieutenant Commander Randall Hindrik, who has the reputation of being a loose cannon, Captain Daniel Adams, who hasn't seen combat in over 5 years and Lieutenant Commander Lucy Alvarez, who doesn't have enough command experience. While the three candidates were acceptable, none were exceptional. For Anderson, there was only one person who was more than suitable for the position but was hesitant to bring her name forward because of her background. He doubted the Ambassador would even consider her. As they were discussing the candidates, Nihlus Kryik, a Turian Spectre, walked in and presented Udina with a datapad.

"Ambassador, Admiral, Captain. I have a candidate that I strongly suggest you consider. In fact, I have already put her name forward to the Council. They're just waiting on your final word." Nihlus made the statement in such a way that left no room for argument and left Udina's office without further word.

After the initial shock wore off, Udina finally looked at the datapad that Nihlus handed him. It was the dossier of none other than Lieutenant Commander Shepard.

"Well, what about Shepard. There's nothing about she was born, just that she was adopted by Hannah Shepard, currently the Executive Officer aboard the SSV Kilimanjaro."

Anderson responded protectively, "Avery was a teenager when she was found and rescued from a facility operated by a terrorist organization. The details of that mission are classified."

"On Elysium, she single-handedly protected the colonists from enemy attack", Hackett contributed.

"She's the only reason Elysium is still standing", Anderson driving the point home.

"We certainly can't question her courage", Udina commented thoughtfully.

Anderson replied, "humanity needs a hero, and Shepard's the best we've got".

The ball was now in Udina's court and he knew it. As he continued to read over her dossier, he knew there was no denying that Shepard was indeed not only the best choice, but the only one. "I'll make the call".


	2. Chapter 2

**Chapter 2**

Captain Anderson was standing at the dock, staring at his new ship, the SSV Normandy SR1. The prototype ship of Turian and Human design was truly a sight to behold. He found himself thinking about Avery, wondering what she will think about the Spectre nomination, or what she might do if she felt she wasn't being given a choice in the matter. And in a twisted way, she really wasn't being presented with a choice. Humanity needed this and Avery is their best chance. Anderson already warned Nihlus of her possible reaction when they tell her the news. On the lighter side, the thought of having Avery and Jeff, a.k.a. Joker, serving on the same ship together made Anderson chuckle to himself. They were nearly thick as thieves and the Normandy's shakedown run was bound to be interesting.

Avery couldn't believe she was going to be Anderson's XO aboard the new, state-of-the art frigate. She had spent half the night reviewing the crew information Anderson had sent her, and was excited to see that her friend Joker was going to be the pilot. There were also a couple other familiar faces: Lieutenant Charles Pressley, Navigator - they met aboard the Agincourt at the end of the Blitz, and Dr. Karin Chakwas, the first doctor to treat her like a person and not a test subject. Avery figured Karin had been picked due to her unique situation, but she was thrilled with the familiarity regardless. Lieutenant Kaidan Alenko, a biotic with an L2 implant, Sentinel. She noticed a special notation about him requiring post-mission checkups with the doctor due to side effects caused by the L2 implant. 'I'll need to ask Karin about it', Avery thought to herself, unfamiliar with the implant as she herself did not have one. Lastly, there was Corporal Jenkins. While not fresh out of boot camp, he was completely green, having never served on a ship or been in any combat situation before.

After showering, Avery put on her dress blue uniform and took a moment to inspect her new rank insignia. With her new position as XO, came a promotion to Commander. Deciding she looked good to go, she grabbed her duffel bags, one containing her special made armor and the other containing her BDUs and other necessities, and headed out to meet Anderson at the docking bay where the Normandy was waiting.

"She's a beautiful ship Sir", Avery spoke as she approached Anderson. He had been so lost in his thoughts, that he didn't notice she was there.

"What have I told you about using that 'Sir' crap with me Avery?", he responded with a smirk.

Avery smiled slightly, "are you ready to get your ass on the ship, or are you just gonna stand there all day Anderson?"

They both ended up laughing at that one and headed towards the Normandy's airlock.

"_The Commanding Officer is aboard. XO Shepard is aboard." _the ship's VI announced.

"Joker! As soon as our guest arrives, get us underway to Eden Prime", Anderson ordered. Not waiting for a response, "Shepard, let's get you squared away and give you a quick tour of the ship."

Joker began his pre-flight checks and wondered who this mystery guest was.


	3. Chapter 3

**Chapter 3**

Avery didn't know what to feel about the idea of becoming a Spectre, despite Anderson's encouragement. But now was not the time to dwell on it. They received the distress call from Eden Prime. A ship of unknown origin landed and the colony came under attack. This was no longer a simple Beacon retrieval.

As soon as their feet hit the ground, Shepard, Alenko and Jenkins drew their weapons, while Alenko also scanned the perimeter for hostiles.

"Area clear, Commander" stated Alenko.

Shepard, in full command mode, responded "Okay, I'll take point. Jenkins, I want you in the middle, eyes open, while Alenko takes up the rear. As the Captain said, getting that Beacon is our number one priority. However, there's too many unknowns, so stay alert and don't do anything stupid. Are we clear?"

Alenko and Jenkins both responded "aye, aye ma'am!"

Moving forward, all was clear. As soon as they saw what would be the first of many dead bodies, Jenkins panicked, as Eden Prime had been his home until he joined the Alliance. Alenko assured him that those responsible would be made to pay, but right now he needed to stay focused on the mission. They came to a clearing and Shepard held up her fist, giving the signal to stop. She sensed something was there, but couldn't find it. Jenkins didn't wait for the signal to move, and before Alenko could stop him, ran past Shepard.

"JENKINS! GET YOUR ASS BACK HERE NOW!" Shepard screamed, but before he could respond to her order, two drones came out of nowhere and opened fire on him. Jenkins screamed in pain as the drones' weapons penetrated his shields, and fell limp to the ground. He never moved again.


	4. Chapter 4

**Chapter 4**

Gunnery Chief Ashley Williams found herself being chased by 2 Geth units, her shields barely holding against their weapon fire. Just as she managed to get herself behind a large rock and ready her assault rifle, she heard an explosion and was showered with pieces of Geth. Not seeing enemies on her HUD display, she stepped out from behind cover.

"Gunnery Chief Ashley Williams of the 212. You guys sure saved my ass".

"Commander Avery Shepard, SSV Normandy. What the hell happened here Chief?"

"It's all a blur ma'am. One minute, we're guarding the dig site while the scientists were preparing the beacon for transport, and the next we're under attack by the Geth".

Shocked, Alenko spoke up, "Geth? Are you sure? They haven't been seen outside the Veil in over two centuries".

"Positive Sir. I think they came for the beacon".

"Where's the rest of your Unit Williams?", Shepard asked.

Shepard saw the sadness in Ashley's eyes as the Gunnery Chief answered. "They're all dead ma'am. Never stood a chance".

Looking Williams square in the eye, Shepard stated firmly, "I know it's all feeling pretty raw right now Williams, but there's nothing you could've done. The anger you're feeling, use it. Avenge your Unit by helping us get to that beacon before those walking trashcans do. Can you do that Williams?"

Stunned by the Commander's tone, Ashley stood there dumbfounded, unable to respond.

Noticing her hesitation, Shepard immediately stepped into Ashley's personal space until they were standing nose to nose. "Gunnery Chief Williams! Can. you. do. that?"

Coming back to herself, Williams snapped to attention and responded with a "yes ma'am!"

On Shepard's order to "move out", they continued down the path, unaware of the horrors that awaited them.


	5. Chapter 5

**Chapter 5**

After dealing with a group of husks, for that was the only way to describe the mindless creatures that had once been human, they found Nihlus laying in his own blood. They were told by Powell, a lazy dock worker who had been napping behind the crates, that it was another Turian who killed Nihlus and he heard the name Saren.

As they were nearing the tram station, Shepard, Alenko and Williams found their path blocked by Geth. Shepard's biotics came to life with a blue and white brilliance, parts of her armor glowing, and Charged into the biggest sythetic in her path. The collision ended in an explosion of raw power, that none remained standing. Williams watched in awe, as she had never seen anything like it before. Alenko, while mesmerized, was also on the verge of freaking out. He was expecting Shepard to collapse after releasing so much energy, but to see her still standing was beyond all belief. When they caught up with her, Alenko was the first to speak.

"Commander, how the hell were you able to do that? I didn't think the L3 implants were that powerful!"

Ashley then questioned, "yeah Commander, and what's up with your armor getting all glowy too?"

Anderson had warned her to expect these kinds of questions. Dr. Chakwas had also tried to help her prepare for such eventuality. Avery had only told one person, Joker, about her abilities and what had been done to her. She met him on Arturus one day, on her way home from having lunch with Dr. Chakwas. What had gotten her attention at first, were two guys laughing maniacally and spewing insults. As soon as she realized they were hurting someone, she pulled them off their victim with her biotics. Joker had already passed out from the pain of his injuries. Later, his parents had thanked Avery profusely and explained about his bone condition called Vrolik Syndrome. When she heard the thugs make jokes about seeing just how brittle his bones were, she thought they were just saying that to be mean, so when she found out about the Vrolik's, Avery wished she had hurt them worse than she did. It didn't take her and Joker long to become friends. She didn't judge him because of his disease and he never thought of her as a freak. Eventually, as their friendship grew, she told him the truth. The possibility of having to explain that to anyone, especially members of her crew, scared her.

"I know you two have questions, but they will have to wait. Right now, we need to stay focused on the mission."

While Williams responded with "yes ma'am", Alenko couldn't leave well enough alone.

"So that's it? No answers? Are you taking something to enhance your abilities?"

Shepard couldn't believe her ears. Even Williams was speechless.

"For fuck's sake Alenko! What is your damn problem?! In case you need to be reminded, we are in the middle of what amounts to a goddamn war zone! So, when I say the questions will have to wait, THEY HAVE TO FUCKING WAIT! AM I CLEAR LIEUTENANT?!"

Shepard didn't wait for Alenko to respond, and Williams prayed she never made Shepard that angry.


	6. Chapter 6

**Chapter 6**

Shepard provided Alenko with barrier support as he difused the bombs, while also assisting Williams with taking out oncoming Geth. Once those tasks were done, they finally reached the beacon. After dealing with a few more husks and Geth, Shepard radioed the Normandy for extraction. The beacon was glowing and Williams commented that it hadn't been doing that earlier. Alenko, curious by the fact that it was Prothean technology, and seemingly functional, approached the beacon for a closer look. But as he got closer, Alenko suddenly found himself surrounded by green light and getting pulled in by the beacon. Noticing this, Shepard pushed past Williams and ran towards him. She grabbed a hold of him around his waist and pulled him hard out of the pay, only to find that she herself was now being pulled in. Williams and Alenko both tried to get to her, but it was too late. The green energy from the beacon had Shepard suspended two feet in the air, with her arms outstretched to the sides. Her mind was being flooded by images of death and destruction, and she could hear their screams. Blood began to trickle down from her nose as she clenched her eyes shut. Shepard was thrown several yards by the beacon's explosion and she knew nothing more.

Dr. Chakwas was waiting for them in the cargo bay with a stretcher. Knowing that Joker would be scared for his friend, she promised to update him on Avery's condition as soon as she knew more. As soon as she was placed on the gurney, Shepard began having a seizure, and her biotics started flaring. Chakwas administered a strong sedative and the convulsions stopped. Shepard was then rushed up to the Med Bay.

Karin began running scans, and noted that Shepard's vitals were eratic, and her brain waves were off the charts. She cleaned the dried blood from under her nose, and went to check her pupils. As the doctor lifted an eyelid, she saw the eye had a green glow. She lifted the other eyelid, and found the same glow. She had no idea what to make of it and continued monitor Shepard's brain functions. While checking for other injuries, she discovered that Shepard's left shoulder was dislocated, likely from when she landed after being thrown by the explosion, and immediately reset it. Finding no other injuries, she kept the scanners running in case anything changed and stepped out of the Med Bay to find Alenko and the other soldier she saw helping him carry Shepard on-board.

She found the soldier sitting by herself at a table in the mess hall, and walked over towards her.

"Hello dear, do you mind if I join you? I saw you help the Lieutenant carry the Commander on-board, but with everything going on, I'm afraid I didn't have the chance to get your name. I'm Dr. Chakwas."

Startled out of her thoughts, "Gunnery Chief Ashley Williams ma'am. How is the Commander doing?"

"A pleasure Chief. The Commander is still unconcious from the sedative I had to give her, which will wear off in a few hours, but I'm not sure when she will wake. There's also some strange symptoms that I can't explain. Can you tell me what happened?"

Williams took a slow deep breath, and noticed Joker walking towards them. As he sat down, she looked to the doctor before answering, not knowing if she should be talking about it in front of him.

Noticing her hesitation, Karin explained, "it's okay Chief. Jeff and Shepard have been close friends for years and he's been worried sick about her."


	7. Chapter 7

**Chapter 7**

"By the time we finally found the beacon, it was glowing, as if it turned itself on or something. Lieutenant Alenko walked towards it to get a closer look and it started pulling him in. Next thing I know, the Commander's running full speed ahead to save him. She managed to pull the Lieutenant out of the way, but ended up trapped by the beacon. We both tried to get to her, but it had her around two feet in the air, and all we could do was stand there and watch. Then something caused the beacon to explode and she was thrown hard."

Five hours later, Dr. Chakwas was checking on Shepard when Joker walked in.

"How's she doing Doc?"

"Well, the sedative wore off about an hour ago, so she's now in a natural sleep. However, there's still no telling when she will wake up."

Joker pulled up a chair and sat down by Shepard's bed. "You need to wake up Av. I need my friend."

A couple hours later, Karin found him asleep in the chair, holding Shepard's hand. She smiled at the tender moment, and was very grateful that Avery had someone in her life, other than herself, Anderson and her mother.

Meanwhile, Alenko was speaking with Anderson in the Captain's quarters. He couldn't wait any longer to say what he felt needed to be said.

"Sir, I think you should know that it is my belief that the Commander is taking something to enhance her biotics."

Anderson's eyes snapped to Alenko. "Lieutenant, on what grounds are you basing such a statement?"

"Sir, the power of her biotics is not natural. The L3 implant is not capable of the amount of power she used on Eden Prime. Even with the best amp on the market, it's just not possible."

"So let me get this straight Lieutenant, you saw Shepard do something you can't possibly understand, so that's the conclusion you jump to? Do you honestly think for one damn minute that I would have picked her, the Hero of the Blitz and the best N7 the Alliance has, as my XO if she has been using drugs?! I have known the Commander for half her life, and so has Dr. Chakwas. Lieutenant, while it's not my story to tell, I will tell you this. Commander Shepard has always been that powerful and is the strongest biotic in the whole damn Alliance. Have you even tried asking her?"

"Yes sir, I did, but the only answer she gave was that the questions had to wait."

"Of course that's what she would have said. A ground mission is not the time or place to ask those kinds of questions. You should know that. I suggest you let the Commander be the one to bring it up. Don't ask anymore questions. In the meantime, go get some rest. Dismissed."

Alenko replied "yes Sir" and left. 'Unbelievable' Anderson thought to himself.


	8. Chapter 8

**Chapter 8**

Shepard opened her eyes slowly, only to be greeted by the bright lights of the Med Bay causing to squeeze her eyes shut and moan at the discomfort.

"Hey Doc, she's waking up!" Joker was excited to see Avery had finally awakened.

Dr. Chakwas noticed Shepard's reaction to the lights and turned them down to make her more comfortable. "How are you feeling Shepard?"

"Like my head's been trampled on by a Krogan". Shepard tried to sit up, but was hit with a wave of dizziness.

"Easy there Shepard, you've been through quite an ordeal. What's the last thing you remember?", Chakwas asked.

Shepard had to think for a moment, as she was having difficulty focusing. "I... I remember Corporal Jenkins being killed, and..."

Joker looked at her worriedly, "Av?"

Shepard tried not to panic when she responded, "I don't know. I woke up here. What happened?"

"It's alright Shepard. With the trauma you endured, some memory loss is normal and is only temporary. You need to rest so you can finish healing", Chakwas spoke soothingly. "I'll give you something for the pain, which will probably make you fall asleep. It will make it easier for you to rest. Don't worry, I'll let the Captain know."

"I've got to head back up to the bridge Av, but I'll be back after my shift. You won't be alone." Joker gave her a light kiss on the forehead before leaving the Med Bay.

The painkillers kicked in fast, and Shepard found it difficult to keep her eyes open.

Anderson was reading over the reports Alenko and Williams gave about what happened on Eden Prime. When his eyes fell upon the mention of Saren's name, his anger began to swell. He barely heard his door open when Dr. Chakwas walked in.

"Doctor, how's Shepard?"

"After nearly 36 hours, the Commander awakened in pain and experienced some dizziness. I'm afraid she is also experiencing some memory loss."

Anderson was startled by the revelation. "How much memory loss?"

"Shepard doesn't remember anything after losing Corporal Jenkins. Whether it was caused by her interaction with the beacon or by it exploding, I do not know."

Pinching the bridge of his nose, "I'll need a copy of your findings to present to Ambassador Udina. He won't be pleased. The reports from Alenko and Williams won't be enough. Shepard will need to be there when we meet with the Council. This will cause a delay, but we don't have a choice. Is there anything that can be done to help Shepard?"

"I will take her to Huerta Memorial and run more specialized scans that I do not have the equipment for on the ship. That will give me a clearer picture of what's going on."

"Do what you need to Doctor. I'll contact Hannah and let her know what's happened. She'll want to be there."

"I'll keep you informed Captain."


End file.
